scholarly journals Conformational Transition of KcsA Gating and the Mechanism of its pH-Dependence

2013 ◽  
Vol 104 (2) ◽  
pp. 25a
Author(s):  
Po-Chao Wen ◽  
Mahmoud Moradi ◽  
Raymond E. Hulse ◽  
Eduardo Perozo ◽  
Emad Tajkhorshid
2014 ◽  
Vol 4 (4) ◽  
pp. 200-206
Author(s):  
C. O. Ehi-Eromosele ◽  
A. Edobor-Osoh ◽  
C. O. Ajanaku ◽  
W. U. Anake ◽  
O. Aladesuyi ◽  
...  

The red blood cell of turkey contains two haemoglobin types, major and minor components. In the present study, the equilibrium constant, Kequ, for the reaction of 5,5′-dithiobis(2-nitrobenzoate), DTNB, with the sulphydryl group of the major turkey aquomethaemoglobin was determined at 25°C as a function of pH. Kequ varies by about 2 to 3 orders of magnitude between pH 5.6 and 9.0 for both haemoglobin [stripped and in the presence of inositol hexakisphosphate (inositol-P6)]. Calculations from the pH dependence of Kequ showed that in the r ⇌ t tertiary conformational transition of aquomethae-moglobin, the t isomer population was 0.26 %. In the presence of inositol-P6, the t isomer population increased to 9.08 %. The results showed that while inositol-P6 increased the relative population of the t tertiary conformation by changing the relative distribution of two protein conformations, it had no effect on Kequ. The effect of Inositol-P6 on the nature and number of groups linked to the DTNB reaction was also determined.


2002 ◽  
Vol 361 (3) ◽  
pp. 547-556 ◽  
Author(s):  
Yoichi MATSUNAGA ◽  
Nobuhiro SAITO ◽  
Akihiro FUJII ◽  
Junichi YOKOTANI ◽  
Tadakazu TAKAKURA ◽  
...  

In the present study we identified the epitopes of antibodies against amyloid β-(1–42)-peptide (Aβ1–42): 4G8 reacted with peptides corresponding to residues 17–21, 6F/3D reacted with peptides corresponding to residues 9–14, and anti 5-10 reacted with peptides corresponding to residues 5–10. The study also yielded some insight into the Aβ1–42 structures resulting from differences in pH. An ELISA study using monoclonal antibodies showed that pH-dependent conformational changes occur in the 6F/3D and 4G8 epitopes modified at pH 4.6, but not in the sequences recognized by anti 1-7 and anti 5-10. This was unique to Aβ1–40 and Aβ1–42 and did not occur with Aβ1–16 or Aβ17–42. The reactivity profile of 4G8 was not affected by blockage of histidine residues of pH-modified Aβ1–40 and Aβ1–42 with diethyl pyrocarbonate; however, the mutant [Gln11]Aβ1–40 abrogated the unique pH-dependence towards 4G8 observed with Aβ1–40. These findings suggest that these epitopes are cryptic at pH4.6, and that Glu11 is responsible for the changes. We suggest that the abnormal folding of 6F/3D epitope affected by pH masked the 4G8 epitope. A study of the binding of metal ions to Aβ1–42 suggested that Cu2+ and Zn2+ induced a conformational transition around the 6F/3D region at pH7.4, but did not affect the region when it was modified at pH4.6. However, Fe2+ had no effect, irrespective of pH. Aβ modified at pH 4.6 appeared to be relatively resistant to proteinase K compared with Aβs modified at pH7.4, and the former might be preferentially internalized and accumulated in a human glial cell. Our findings suggest the importance of microenvironmental changes, such as pH, in the early stage of formation of Aβ aggregates in the glial cell.


1999 ◽  
Vol 338 (1) ◽  
pp. 235-239 ◽  
Author(s):  
Manuel MORILLAS ◽  
Martin L. GOBLE ◽  
Richard VIRDEN

Penicillin G acylase catalysed the hydrolysis of 4-nitrophenyl acetate with a kcat of 0.8 s-1 and a Km of 10 µM at pH 7.5 and 20 °C. Results from stopped-flow experiments fitted a dissociation constant of 0.16 mM for the Michaelis complex, formation of an acetyl enzyme with a rate constant of 32 s-1 and a subsequent deacylation step with a rate constant of 0.81 s-1. Non-linear Van't Hoff and Arrhenius plots for these parameters, measured at pH 7.5, may be partly explained by a conformational transition affecting catalytic groups, but a linear Arrhenius plot for the ratio of the rate constant for acylation relative to KS was consistent with energy-compensation between the binding of the substrate and catalysis of the formation of the transition state. At 20 °C, the pH-dependence of kcat was similar to that of kcat/Km, indicating that formation of the acyl-enzyme did not affect the pKa values (6.5 and 9.0) of an acidic and basic group in the active enzyme. The heats of ionization deduced from values of pKa for kcat, which measures the rate of deacylation, are consistent with α-amino and guanidinium groups whose pKa values are decreased in a non-polar environment. It is proposed that, for catalytic activity, the α-amino group of the catalytic SerB1 and the guanidinium group of ArgB263 are required in neutral and protonated states respectively.


Diabetes ◽  
1987 ◽  
Vol 36 (3) ◽  
pp. 261-264 ◽  
Author(s):  
E. Helmerhorst ◽  
G. B. Stokes

2017 ◽  
Author(s):  
Jana Shen ◽  
Zhi Yue ◽  
Helen Zgurskaya ◽  
Wei Chen

AcrB is the inner-membrane transporter of E. coli AcrAB-TolC tripartite efflux complex, which plays a major role in the intrinsic resistance to clinically important antibiotics. AcrB pumps a wide range of toxic substrates by utilizing the proton gradient between periplasm and cytoplasm. Crystal structures of AcrB revealed three distinct conformational states of the transport cycle, substrate access, binding and extrusion, or loose (L), tight (T) and open (O) states. However, the specific residue(s) responsible for proton binding/release and the mechanism of proton-coupled conformational cycling remain controversial. Here we use the newly developed membrane hybrid-solvent continuous constant pH molecular dynamics technique to explore the protonation states and conformational dynamics of the transmembrane domain of AcrB. Simulations show that both Asp407 and Asp408 are deprotonated in the L/T states, while only Asp408 is protonated in the O state. Remarkably, release of a proton from Asp408 in the O state results in large conformational changes, such as the lateral and vertical movement of transmembrane helices as well as the salt-bridge formation between Asp408 and Lys940 and other sidechain rearrangements among essential residues.Consistent with the crystallographic differences between the O and L protomers, simulations offer dynamic details of how proton release drives the O-to-L transition in AcrB and address the controversy regarding the proton/drug stoichiometry. This work offers a significant step towards characterizing the complete cycle of proton-coupled drug transport in AcrB and further validates the membrane hybrid-solvent CpHMD technique for studies of proton-coupled transmembrane proteins which are currently poorly understood. <p><br></p>


2019 ◽  
Author(s):  
Adrian Roitberg ◽  
Pancham Lal Gupta

<div>Human Glycinamide ribonucleotide transformylase (GAR Tfase), a regulatory enzyme in the de novo purine biosynthesis pathway, has been established as an anti-cancer target. GAR Tfase catalyzes the formyl transfer reaction from the folate cofactor to the GAR ligand. In the present work, we study E. coli GAR Tfase, which has high sequence similarity with the human GAR Tfase with most functional residues conserved. E. coli GAR Tfase exhibits structural changes and the binding of ligands that varies with pH which leads to change the rate of the formyl transfer reaction in a pH-dependent manner. Thus, the inclusion of pH becomes essential for the study of its catalytic mechanism. Experimentally, the pH-dependence of the kinetic parameter kcat is measured to evaluate the pH-range of enzymatic activity. However, insufficient information about residues governing the pH-effects on the catalytic activity leads to ambiguous assignments of the general acid and base catalysts and consequently its catalytic mechanism. In the present work, we use pH-replica exchange molecular dynamics (pH-REMD) simulations to study the effects of pH on E. coli GAR Tfase enzyme. We identify the titratable residues governing the pH-dependent conformational changes in the system. Furthermore, we filter out the protonation states which are essential in maintaining the structural integrity, keeping the ligands bound and assisting the catalysis. We reproduce the experimental pH-activity curve by computing the population of key protonation states. Moreover, we provide a detailed description of residues governing the acidic and basic limbs of the pH-activity curve.</div>


1961 ◽  
Vol 26 (1) ◽  
pp. 141-155 ◽  
Author(s):  
S. Ono ◽  
M. Takagi ◽  
T. Wasa
Keyword(s):  

1986 ◽  
Vol 51 (8) ◽  
pp. 1665-1670 ◽  
Author(s):  
Petr Kuzmič ◽  
Libuše Pavlíčková ◽  
Jiří Velek ◽  
Milan Souček
Keyword(s):  

Irradiation of 3,4-dimethoxy-1-nitrobenzene in the presence of butylamine leads to the formation of both possible photosubstitution products, i.e., 2-methoxy-4-nitro-N-butylaniline and 2-methoxy-5-nitro-N-butylaniline with the predominance of the latter. Regioselectivity of the reaction as measured by molar ratio of the two isomeric products varies with pH of the solution, ranging from 3 : 1 at pH 10 to 12. The results are discussed in view of possible use of 3,4-dimethoxy-1-nitrobenzene moiety as a lysine-directed photoaffinity probe.


1989 ◽  
Vol 54 (1) ◽  
pp. 64-69 ◽  
Author(s):  
Roland Meier ◽  
Gerhard Werner ◽  
Matthias Otto

Electrochemical oxidation of [V(IV)O(nta)(H2O)]- (H3nta nitrilotriacetic acid) was studied in aqueous solution by means of cyclic voltammetry, differential pulse polarography, and current sampled DC polarography on mercury as electrode material. In the pH-range under study (5.5-9.0) the corresponding V(V) complex is produced by one-electron oxidation of the parent V(IV) species. The oxidation product is stable within the time scale of cyclic voltammetry. The evaluation of the pH-dependence of the half-wave potentials leads to a pKa value for [V(IV)O(nta)(H2O)]- which is in a good agreement with previous determinations. The measured value for E1/2 is very close to the formal potential E0 calculated via the Nernst equation on the basis of known literature values for log Kox and log Kred, the complex stability constants for the oxidized and reduced form, respectively.


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